RetrogeneDB ID: retro_bole_25

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C1:13401318..13402347(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo1g046420
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo3g021260
• Aliases: None
• Description: None

Sequence

>retro_bole_25
ATGAGTACACGTTATTCAACTCAACTGCAATCATCAGCCATTACATCCATCACCGTCTCCTCATCTTCTTCCTTAGACAC
CACTCCGCGGGATGATGATAACACTCACATGACTGCATCTTCCAACGCTCGCGTTAACTCTCCATCATCCTTCTTGATAA
GACTTGCAATGCGGGTATCTAGAGCAAGGTGGTTCATTTTCTTGAGAAGAGTGTTTCATTACCAGAACGGTTCAAGATCC
GATCTTGGCGCCAACCCTTTGGAGTCAACCACTTGGATGATATCGGAGCTCATCGCTTTACTCGTACAGATCACTGTGAT
CACATTCACACTAGCTTTGTCCAAGAACGAGCGGCCTATTTGGCCTGTGAGGCTATGGATCACCGGGTACAACGTCGGAT
GTCTCCTCAGTCTGATGATATTATACGGCCGGTACCGTCAGCAAGACGTTAGCCAAAGCAATGGGTTTACCTTTGGTGAT
ATTGAGCAGCAGCAACAGAGAAGCAGAGAAGAGACCAGGTGCTCGCATTTGATGAACAGATGCAGGACATTGCTGGAACT
CTTCTTTGCGATATGGTTTGTGATAGGAAACGTATGGGTGTTTGATTCTCGGTTCGGTTCTTTCCACTATGCTCCAAGCC
TTCATGTCCTCTGCATCTCTCTTCTCGCTTGGAACGCTCTCTGCTACTCCTTCCCGTTTCTTCTCTTCCTCCTGCTATGT
TGTGTTGTGCCTCTCATTAGTAGCTTCCTAGGCTACAACATGAACATTGGATCCTCGGAGAAAGGAGCTTCAGATGACCA
AATCTCTAGTCTCCCAAGCTGGAAGTACAAACTCATCGACGAAACATCTGATTCTGATTCTTCTCACGCAAGCAATGATC
CGGAGTGTTGCATATGTTTGGCGAAGTACAAAGATAAAGAAGAAGTGAGAAAGCTACCGTGTTCGCATAGGTTTCATGTA
AAATGCGTAGATCAATGGCTTCGTATTATCTCGTCTTGTCCTCTCTGCAAACAAGATCTCCCCAACTAA

Alignment

ORF - retro_bole_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.38 %
• Parental protein coverage: 87.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFYLRFAMRVSRARWFIFLRRVFHYQNGSRSDLGSNPFNSSTWMMSELIALLVQLTVITLTLAISKEERP
          SF..R.AMRVSRARWFIFLRRVFHYQNGSRSDLG.NP..S.TWM.SELIALLVQ.TVIT.TLA.SK.ERP
Retrocopy SFLIRLAMRVSRARWFIFLRRVFHYQNGSRSDLGANPLESTTWMISELIALLVQITVITFTLALSKNERP

Parental  VWPVRLWITGYDVGCLLSLMLLYGRFRQ--LNQGNWFV--DIEQQH-RGRDETRSSHLMNKCRTSLELFF
          .WPVRLWITGY.VGCLLSLM.LYGR.RQ....Q.N.F...DIEQQ..R.R.ETR.SHLMN.CRT.LELFF
Retrocopy IWPVRLWITGYNVGCLLSLMILYGRYRQQDVSQSNGFTFGDIEQQQQRSREETRCSHLMNRCRTLLELFF

Parental  AIWFVVGNVWVFDSRFGSFNHAPNLHVLCVSLLSWNALCYSFPFLLFLFLCCLVPLVSSLLGYNMNMGSS
          AIWFV.GNVWVFDSRFGSF..AP.LHVLC.SLL.WNALCYSFPFLLFL.LCC.VPL.SS.LGYNMN.GSS
Retrocopy AIWFVIGNVWVFDSRFGSFHYAPSLHVLCISLLAWNALCYSFPFLLFLLLCCVVPLISSFLGYNMNIGSS

Parental  DRGASDDQISSLPSWKHKRADDNA-SDSAPKTDDPECCICLAKYKDKEEVRKLPCSHKFHLKCVDQWLRI
          ..GASDDQISSLPSWK.K..D....SDS.....DPECCICLAKYKDKEEVRKLPCSH.FH.KCVDQWLRI
Retrocopy EKGASDDQISSLPSWKYKLIDETSDSDSSHASNDPECCICLAKYKDKEEVRKLPCSHRFHVKCVDQWLRI

Parental  ISCCPLCKQDL
          IS.CPLCKQDL
Retrocopy ISSCPLCKQDL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Brassica oleracea was not studied using RNA-Seq expression data.

ChIP-Seq

Brassica oleracea was not studied using ChIP-Seq data.

EST

Brassica oleracea was not studied using EST data.

TSS

Brassica oleracea was not studied using FANTOM5 data.

Lab

retro_bole_25 was not experimentally validated.

Homology

Retrocopy orthology:

Brassica oleracea does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo3g021260	1 retrocopy	retro_bole_25 ,
Brassica rapa	Bra028950	1 retrocopy	retro_brap_17,